MultiQC Report

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Report generated on 2019-09-11, 14:50 based on data in: /lutra/proj/uppoff2019006/uppstore2018168/P12108_results

General Statistics

Showing ³⁷⁸/₃₇₈ rows and ⁷/₉ columns.

Sample Name	% Aligned	M Aligned	% Dropped	% rRNA	% Dups	% GC	Length	% Failed	M Seqs
P12108_101_S1_L001_R1_001			0.6%	2.9%	53.2%	44%	151 bp	25%	10.2
P12108_101_S1_L001_R2_001					50.1%	44%	151 bp	33%	10.7
P12108_101_S1_L001_sortmerna_trimmomatic	82.1%	6.8
P12108_102_S2_L001_R1_001			0.7%	4.7%	52.7%	44%	151 bp	25%	10.7
P12108_102_S2_L001_R2_001					47.4%	43%	151 bp	33%	11.6
P12108_102_S2_L001_sortmerna_trimmomatic	76.5%	6.4
P12108_103_S3_L001_R1_001			0.7%	5.0%	52.6%	44%	151 bp	25%	10.2
P12108_103_S3_L001_R2_001					47.7%	44%	151 bp	33%	11.1
P12108_103_S3_L001_sortmerna_trimmomatic	75.3%	5.9
P12108_104_S4_L001_R1_001			0.7%	5.2%	44.7%	44%	151 bp	25%	9.0
P12108_104_S4_L001_R2_001					44.8%	44%	151 bp	42%	9.8
P12108_104_S4_L001_sortmerna_trimmomatic	76.0%	5.2
P12108_105_S5_L001_R1_001			0.7%	3.2%	53.5%	44%	151 bp	25%	13.2
P12108_105_S5_L001_R2_001					48.7%	44%	151 bp	25%	13.9
P12108_105_S5_L001_sortmerna_trimmomatic	77.9%	7.9
P12108_106_S6_L001_R1_001			0.6%	4.1%	51.9%	44%	151 bp	17%	11.4
P12108_106_S6_L001_R2_001					46.5%	43%	151 bp	25%	12.3
P12108_106_S6_L001_sortmerna_trimmomatic	76.9%	7.4
P12108_107_S7_L001_R1_001			0.7%	4.4%	45.7%	43%	151 bp	17%	12.0
P12108_107_S7_L001_R2_001					45.2%	43%	151 bp	33%	13.0
P12108_107_S7_L001_sortmerna_trimmomatic	77.4%	7.3
P12108_108_S8_L001_R1_001			0.6%	5.9%	43.6%	43%	151 bp	8%	9.6
P12108_108_S8_L001_R2_001					38.6%	43%	151 bp	33%	10.6
P12108_108_S8_L001_sortmerna_trimmomatic	77.7%	6.1
P12108_109_S9_L001_R1_001			0.6%	5.0%	43.9%	43%	151 bp	17%	10.9
P12108_109_S9_L001_R2_001					43.7%	43%	151 bp	33%	11.9
P12108_109_S9_L001_sortmerna_trimmomatic	78.4%	6.9
P12108_110_S10_L001_R1_001			0.7%	4.7%	45.8%	43%	151 bp	25%	13.2
P12108_110_S10_L001_R2_001					45.8%	43%	151 bp	42%	14.3
P12108_110_S10_L001_sortmerna_trimmomatic	78.0%	8.1
P12108_111_S11_L001_R1_001			0.6%	3.6%	43.0%	44%	151 bp	17%	9.8
P12108_111_S11_L001_R2_001					43.5%	44%	151 bp	25%	10.3
P12108_111_S11_L001_sortmerna_trimmomatic	80.4%	6.4
P12108_112_S12_L001_R1_001			0.6%	4.6%	43.6%	44%	151 bp	17%	9.5
P12108_112_S12_L001_R2_001					43.7%	44%	151 bp	33%	10.3
P12108_112_S12_L001_sortmerna_trimmomatic	76.8%	5.9
P12108_113_S13_L001_R1_001			0.8%	6.1%	50.7%	44%	151 bp	25%	11.0
P12108_113_S13_L001_R2_001					45.9%	44%	151 bp	42%	12.2
P12108_113_S13_L001_sortmerna_trimmomatic	73.5%	5.9
P12108_114_S14_L001_R1_001			0.6%	4.6%	52.2%	44%	151 bp	17%	12.3
P12108_114_S14_L001_R2_001					47.1%	43%	151 bp	25%	13.3
P12108_114_S14_L001_sortmerna_trimmomatic	79.1%	8.2
P12108_115_S15_L001_R1_001			0.6%	3.2%	52.1%	44%	151 bp	25%	13.8
P12108_115_S15_L001_R2_001					47.8%	44%	151 bp	17%	14.5
P12108_115_S15_L001_sortmerna_trimmomatic	80.0%	8.9
P12108_116_S16_L001_R1_001			0.7%	4.0%	43.5%	43%	151 bp	17%	11.1
P12108_116_S16_L001_R2_001					43.3%	43%	151 bp	33%	11.8
P12108_116_S16_L001_sortmerna_trimmomatic	77.4%	6.5
P12108_117_S17_L001_R1_001			0.6%	5.1%	41.9%	43%	151 bp	8%	10.9
P12108_117_S17_L001_R2_001					42.6%	43%	151 bp	17%	11.8
P12108_117_S17_L001_sortmerna_trimmomatic	80.7%	7.3
P12108_118_S18_L001_R1_001			0.6%	6.5%	50.6%	44%	151 bp	17%	12.8
P12108_118_S18_L001_R2_001					45.5%	43%	151 bp	33%	14.3
P12108_118_S18_L001_sortmerna_trimmomatic	78.1%	8.2
P12108_119_S19_L001_R1_001			0.6%	4.8%	49.1%	43%	151 bp	17%	12.6
P12108_119_S19_L001_R2_001					46.2%	43%	151 bp	25%	13.5
P12108_119_S19_L001_sortmerna_trimmomatic	81.0%	8.0
P12108_120_S20_L001_R1_001			0.6%	7.5%	43.7%	43%	151 bp	25%	11.2
P12108_120_S20_L001_R2_001					44.6%	44%	151 bp	42%	12.6
P12108_120_S20_L001_sortmerna_trimmomatic	78.2%	6.9
P12108_121_S21_L001_R1_001			0.6%	7.0%	44.6%	43%	151 bp	25%	13.3
P12108_121_S21_L001_R2_001					45.0%	43%	151 bp	42%	14.9
P12108_121_S21_L001_sortmerna_trimmomatic	77.7%	8.1
P12108_122_S22_L001_R1_001			0.6%	5.3%	43.8%	43%	151 bp	8%	11.2
P12108_122_S22_L001_R2_001					44.4%	43%	151 bp	17%	12.1
P12108_122_S22_L001_sortmerna_trimmomatic	81.0%	7.6
P12108_123_S23_L001_R1_001			0.6%	5.6%	48.9%	44%	151 bp	8%	11.7
P12108_123_S23_L001_R2_001					45.7%	43%	151 bp	17%	12.7
P12108_123_S23_L001_sortmerna_trimmomatic	80.5%	7.8
P12108_124_S24_L001_R1_001			0.6%	6.1%	42.4%	43%	151 bp	17%	10.7
P12108_124_S24_L001_R2_001					43.0%	43%	151 bp	42%	11.8
P12108_124_S24_L001_sortmerna_trimmomatic	78.4%	6.7
P12108_125_S25_L001_R1_001			0.6%	9.9%	51.6%	44%	151 bp	25%	10.4
P12108_125_S25_L001_R2_001					47.1%	44%	151 bp	33%	12.2
P12108_125_S25_L001_sortmerna_trimmomatic	79.4%	6.6
P12108_126_S26_L001_R1_001			0.6%	8.3%	52.0%	44%	151 bp	25%	13.1
P12108_126_S26_L001_R2_001					52.0%	44%	151 bp	42%	14.9
P12108_126_S26_L001_sortmerna_trimmomatic	80.1%	8.5
P12108_127_S27_L001_R1_001			0.6%	7.5%	52.1%	44%	151 bp	25%	12.5
P12108_127_S27_L001_R2_001					48.3%	44%	151 bp	42%	14.0
P12108_127_S27_L001_sortmerna_trimmomatic	79.4%	7.9
P12108_128_S28_L001_R1_001			0.6%	8.3%	52.4%	44%	151 bp	33%	11.1
P12108_128_S28_L001_R2_001					52.2%	44%	151 bp	50%	12.7
P12108_128_S28_L001_sortmerna_trimmomatic	79.5%	6.8
P12108_129_S29_L001_R1_001			0.5%	8.9%	57.5%	45%	151 bp	17%	12.7
P12108_129_S29_L001_R2_001					56.3%	45%	151 bp	25%	14.3
P12108_129_S29_L001_sortmerna_trimmomatic	82.5%	8.7
P12108_130_S30_L001_R1_001			0.6%	6.9%	55.3%	44%	151 bp	25%	12.8
P12108_130_S30_L001_R2_001					55.1%	44%	151 bp	33%	14.2
P12108_130_S30_L001_sortmerna_trimmomatic	81.5%	8.4
P12108_131_S31_L001_R1_001			0.6%	9.4%	51.7%	44%	151 bp	25%	10.6
P12108_131_S31_L001_R2_001					52.3%	44%	151 bp	50%	12.2
P12108_131_S31_L001_sortmerna_trimmomatic	80.8%	6.8
P12108_132_S32_L001_R1_001			0.6%	7.5%	51.5%	44%	151 bp	25%	10.5
P12108_132_S32_L001_R2_001					51.6%	44%	151 bp	33%	11.8
P12108_132_S32_L001_sortmerna_trimmomatic	80.1%	6.8
P12108_133_S33_L001_R1_001			0.6%	7.3%	51.6%	45%	151 bp	25%	9.4
P12108_133_S33_L001_R2_001					51.7%	45%	151 bp	33%	10.6
P12108_133_S33_L001_sortmerna_trimmomatic	81.0%	6.2
P12108_134_S34_L001_R1_001			0.6%	6.8%	56.2%	44%	151 bp	17%	14.3
P12108_134_S34_L001_R2_001					52.3%	44%	151 bp	25%	15.8
P12108_134_S34_L001_sortmerna_trimmomatic	81.0%	9.5
P12108_135_S35_L001_R1_001			0.7%	6.0%	60.6%	45%	151 bp	25%	14.0
P12108_135_S35_L001_R2_001					55.3%	45%	151 bp	33%	15.4
P12108_135_S35_L001_sortmerna_trimmomatic	79.6%	8.9
P12108_136_S36_L001_R1_001			0.7%	8.6%	48.2%	44%	151 bp	17%	11.3
P12108_136_S36_L001_R2_001					48.9%	44%	151 bp	33%	12.9
P12108_136_S36_L001_sortmerna_trimmomatic	79.9%	7.2
P12108_137_S37_L001_R1_001			0.7%	9.3%	55.1%	44%	151 bp	33%	10.7
P12108_137_S37_L001_R2_001					54.1%	44%	151 bp	42%	12.6
P12108_137_S37_L001_sortmerna_trimmomatic	79.9%	6.5
P12108_138_S38_L001_R1_001			0.7%	6.8%	56.0%	44%	151 bp	25%	12.9
P12108_138_S38_L001_R2_001					55.9%	44%	151 bp	33%	14.3
P12108_138_S38_L001_sortmerna_trimmomatic	81.6%	8.4
P12108_139_S39_L001_R1_001			0.6%	6.4%	52.1%	44%	151 bp	17%	11.6
P12108_139_S39_L001_R2_001					49.4%	44%	151 bp	17%	12.7
P12108_139_S39_L001_sortmerna_trimmomatic	81.7%	7.9
P12108_140_S40_L001_R1_001			0.6%	6.8%	52.9%	45%	151 bp	25%	10.4
P12108_140_S40_L001_R2_001					52.9%	45%	151 bp	42%	11.6
P12108_140_S40_L001_sortmerna_trimmomatic	79.7%	6.6
P12108_141_S41_L001_R1_001			0.6%	8.3%	53.7%	44%	151 bp	25%	12.1
P12108_141_S41_L001_R2_001					53.2%	44%	151 bp	50%	13.8
P12108_141_S41_L001_sortmerna_trimmomatic	79.9%	7.6
P12108_142_S42_L001_R1_001			0.6%	7.5%	58.2%	45%	151 bp	25%	15.3
P12108_142_S42_L001_R2_001					55.9%	45%	151 bp	33%	17.0
P12108_142_S42_L001_sortmerna_trimmomatic	81.7%	9.9
P12108_143_S43_L001_R1_001			0.6%	5.2%	52.3%	44%	151 bp	25%	16.0
P12108_143_S43_L001_R2_001					49.8%	43%	151 bp	25%	17.3
P12108_143_S43_L001_sortmerna_trimmomatic	79.6%	10.4
P12108_144_S44_L001_R1_001			0.6%	6.6%	45.6%	43%	151 bp	17%	11.7
P12108_144_S44_L001_R2_001					46.1%	43%	151 bp	25%	13.0
P12108_144_S44_L001_sortmerna_trimmomatic	78.5%	7.3
P12108_145_S45_L001_R1_001			0.7%	6.9%	50.7%	44%	151 bp	33%	14.4
P12108_145_S45_L001_R2_001					46.1%	43%	151 bp	42%	16.2
P12108_145_S45_L001_sortmerna_trimmomatic	75.9%	8.2
P12108_146_S46_L001_R1_001			0.6%	7.1%	44.8%	43%	151 bp	25%	12.7
P12108_146_S46_L001_R2_001					44.9%	42%	151 bp	42%	14.3
P12108_146_S46_L001_sortmerna_trimmomatic	77.0%	7.7
P12108_147_S47_L001_R1_001			0.6%	6.1%	46.6%	43%	151 bp	17%	13.8
P12108_147_S47_L001_R2_001					47.2%	43%	151 bp	25%	15.0
P12108_147_S47_L001_sortmerna_trimmomatic	79.2%	8.8
P12108_148_S48_L001_R1_001			0.7%	6.2%	47.3%	43%	151 bp	17%	11.2
P12108_148_S48_L001_R2_001					43.4%	43%	151 bp	42%	12.5
P12108_148_S48_L001_sortmerna_trimmomatic	77.2%	6.7
P12108_149_S49_L001_R1_001			0.6%	6.8%	46.4%	44%	151 bp	8%	9.9
P12108_149_S49_L001_R2_001					42.6%	43%	151 bp	33%	11.0
P12108_149_S49_L001_sortmerna_trimmomatic	78.5%	6.4
P12108_150_S50_L001_R1_001			0.6%	7.6%	54.3%	44%	151 bp	25%	15.9
P12108_150_S50_L001_R2_001					49.1%	43%	151 bp	33%	18.0
P12108_150_S50_L001_sortmerna_trimmomatic	77.6%	9.8
P12108_151_S51_L001_R1_001			0.6%	6.4%	47.6%	43%	151 bp	8%	15.5
P12108_151_S51_L001_R2_001					48.3%	43%	151 bp	17%	17.0
P12108_151_S51_L001_sortmerna_trimmomatic	79.7%	10.1
P12108_152_S52_L001_R1_001			0.7%	5.4%	47.9%	43%	151 bp	25%	13.7
P12108_152_S52_L001_R2_001					47.6%	43%	151 bp	42%	15.0
P12108_152_S52_L001_sortmerna_trimmomatic	77.3%	8.2
P12108_153_S53_L001_R1_001			0.7%	5.1%	48.6%	43%	151 bp	17%	15.5
P12108_153_S53_L001_R2_001					48.3%	43%	151 bp	42%	16.9
P12108_153_S53_L001_sortmerna_trimmomatic	77.7%	9.3
P12108_154_S54_L001_R1_001			0.7%	4.2%	55.1%	43%	151 bp	25%	15.9
P12108_154_S54_L001_R2_001					51.5%	43%	151 bp	33%	17.0
P12108_154_S54_L001_sortmerna_trimmomatic	78.9%	9.8
P12108_155_S55_L001_R1_001			0.8%	4.7%	48.7%	44%	151 bp	17%	14.7
P12108_155_S55_L001_R2_001					48.9%	44%	151 bp	25%	15.8
P12108_155_S55_L001_sortmerna_trimmomatic	78.9%	8.3
P12108_156_S56_L001_R1_001			0.7%	5.5%	50.0%	44%	151 bp	17%	11.8
P12108_156_S56_L001_R2_001					45.1%	43%	151 bp	42%	13.0
P12108_156_S56_L001_sortmerna_trimmomatic	77.3%	7.1
P12108_157_S69_L002_R1_001			0.7%	6.2%	42.8%	44%	151 bp	17%	7.6
P12108_157_S69_L002_R2_001					37.7%	43%	151 bp	33%	8.5
P12108_157_S69_L002_sortmerna_trimmomatic	78.5%	4.7
P12108_158_S70_L002_R1_001			0.8%	6.0%	48.9%	44%	151 bp	17%	10.2
P12108_158_S70_L002_R2_001					43.3%	43%	151 bp	42%	11.3
P12108_158_S70_L002_sortmerna_trimmomatic	77.8%	6.2
P12108_159_S71_L002_R1_001			0.7%	4.6%	44.5%	43%	151 bp	8%	11.2
P12108_159_S71_L002_R2_001					44.8%	43%	151 bp	17%	12.0
P12108_159_S71_L002_sortmerna_trimmomatic	80.3%	7.4
P12108_160_S72_L002_R1_001			0.8%	4.5%	49.1%	44%	151 bp	17%	11.4
P12108_160_S72_L002_R2_001					45.5%	43%	151 bp	25%	12.3
P12108_160_S72_L002_sortmerna_trimmomatic	79.3%	7.1
P12108_161_S73_L002_R1_001			0.7%	5.5%	46.4%	43%	151 bp	25%	10.6
P12108_161_S73_L002_R2_001					46.1%	43%	151 bp	42%	11.7
P12108_161_S73_L002_sortmerna_trimmomatic	76.1%	6.4
P12108_162_S74_L002_R1_001			0.8%	3.8%	52.4%	44%	151 bp	25%	13.9
P12108_162_S74_L002_R2_001					47.6%	43%	151 bp	25%	14.8
P12108_162_S74_L002_sortmerna_trimmomatic	79.0%	8.4
P12108_163_S75_L002_R1_001			0.8%	4.2%	48.4%	43%	151 bp	17%	14.1
P12108_163_S75_L002_R2_001					48.1%	43%	151 bp	25%	15.2
P12108_163_S75_L002_sortmerna_trimmomatic	78.2%	8.8
P12108_201_S76_L002_R1_001			1.1%	5.3%	45.6%	43%	151 bp	17%	13.6
P12108_201_S76_L002_R2_001					45.3%	43%	151 bp	42%	15.0
P12108_201_S76_L002_sortmerna_trimmomatic	76.5%	6.9
P12108_202_S77_L002_R1_001			0.7%	4.7%	58.7%	44%	151 bp	25%	24.4
P12108_202_S77_L002_R2_001					51.9%	43%	151 bp	50%	26.5
P12108_202_S77_L002_sortmerna_trimmomatic	77.8%	7.4
P12108_203_S78_L002_R1_001			0.7%	5.2%	64.0%	44%	151 bp	17%	29.8
P12108_203_S78_L002_R2_001					57.4%	43%	151 bp	42%	32.5
P12108_203_S78_L002_sortmerna_trimmomatic	77.0%	18.3
P12108_204_S79_L002_R1_001			0.8%	4.1%	52.5%	44%	151 bp	25%	19.2
P12108_204_S79_L002_R2_001					52.3%	44%	151 bp	33%	20.4
P12108_204_S79_L002_sortmerna_trimmomatic	79.5%	11.8
P12108_205_S80_L002_R1_001			0.8%	4.1%	51.2%	44%	151 bp	25%	14.4
P12108_205_S80_L002_R2_001					51.0%	44%	151 bp	33%	15.3
P12108_205_S80_L002_sortmerna_trimmomatic	77.3%	8.6
P12108_206_S81_L002_R1_001			0.8%	5.4%	48.0%	44%	151 bp	17%	12.2
P12108_206_S81_L002_R2_001					47.9%	44%	151 bp	42%	13.4
P12108_206_S81_L002_sortmerna_trimmomatic	75.6%	7.0
P12108_207_S82_L002_R1_001			0.7%	3.9%	51.1%	44%	151 bp	25%	14.0
P12108_207_S82_L002_R2_001					46.4%	43%	151 bp	25%	14.9
P12108_207_S82_L002_sortmerna_trimmomatic	79.6%	9.0
P12108_208_S83_L002_R1_001			0.7%	4.1%	49.0%	43%	151 bp	17%	16.7
P12108_208_S83_L002_R2_001					48.7%	43%	151 bp	25%	17.9
P12108_208_S83_L002_sortmerna_trimmomatic	79.6%	10.6
P12108_209_S84_L002_R1_001			0.7%	3.9%	53.5%	44%	151 bp	25%	16.2
P12108_209_S84_L002_R2_001					47.8%	43%	151 bp	33%	17.3
P12108_209_S84_L002_sortmerna_trimmomatic	77.1%	10.0
P12108_210_S85_L002_R1_001			0.7%	5.4%	50.7%	43%	151 bp	25%	19.6
P12108_210_S85_L002_R2_001					50.2%	43%	151 bp	50%	21.6
P12108_210_S85_L002_sortmerna_trimmomatic	78.7%	12.1
P12108_211_S86_L002_R1_001			0.7%	4.3%	57.9%	43%	151 bp	25%	28.7
P12108_211_S86_L002_R2_001					57.2%	43%	151 bp	33%	30.9
P12108_211_S86_L002_sortmerna_trimmomatic	78.0%	18.0
P12108_212_S87_L002_R1_001			0.6%	4.3%	46.1%	43%	151 bp	8%	12.4
P12108_212_S87_L002_R2_001					46.1%	43%	151 bp	17%	13.3
P12108_212_S87_L002_sortmerna_trimmomatic	80.3%	8.5
P12108_213_S88_L002_R1_001			0.9%	6.2%	50.7%	44%	151 bp	33%	10.3
P12108_213_S88_L002_R2_001					44.5%	43%	151 bp	42%	11.6
P12108_213_S88_L002_sortmerna_trimmomatic	77.8%	5.6
P12108_214_S89_L002_R1_001			0.7%	4.1%	49.1%	44%	151 bp	17%	14.9
P12108_214_S89_L002_R2_001					49.0%	44%	151 bp	25%	16.0
P12108_214_S89_L002_sortmerna_trimmomatic	78.9%	9.1
P12108_215_S90_L002_R1_001			0.8%	5.8%	50.5%	44%	151 bp	25%	10.4
P12108_215_S90_L002_R2_001					44.9%	43%	151 bp	42%	11.6
P12108_215_S90_L002_sortmerna_trimmomatic	76.6%	6.1
P12108_216_S91_L002_R1_001			0.7%	3.0%	44.3%	43%	151 bp	17%	14.8
P12108_216_S91_L002_R2_001					43.9%	43%	151 bp	25%	15.6
P12108_216_S91_L002_sortmerna_trimmomatic	78.7%	9.2
P12108_217_S92_L002_R1_001			0.8%	6.1%	53.1%	44%	151 bp	25%	18.3
P12108_217_S92_L002_R2_001					48.5%	43%	151 bp	42%	20.2
P12108_217_S92_L002_sortmerna_trimmomatic	78.8%	11.4
P12108_218_S93_L002_R1_001			0.7%	4.4%	54.2%	44%	151 bp	25%	17.0
P12108_218_S93_L002_R2_001					47.7%	43%	151 bp	33%	18.5
P12108_218_S93_L002_sortmerna_trimmomatic	77.3%	10.5
P12108_219_S94_L002_R1_001			0.8%	7.0%	46.6%	44%	151 bp	17%	12.0
P12108_219_S94_L002_R2_001					42.0%	43%	151 bp	42%	13.5
P12108_219_S94_L002_sortmerna_trimmomatic	78.6%	6.9
P12108_220_S95_L002_R1_001			0.7%	5.4%	47.4%	44%	151 bp	17%	12.8
P12108_220_S95_L002_R2_001					44.8%	44%	151 bp	25%	13.8
P12108_220_S95_L002_sortmerna_trimmomatic	81.4%	8.5
P12108_221_S96_L002_R1_001			0.7%	4.7%	48.2%	44%	151 bp	17%	9.7
P12108_221_S96_L002_R2_001					42.2%	43%	151 bp	42%	10.7
P12108_221_S96_L002_sortmerna_trimmomatic	78.4%	6.0
P12108_222_S97_L002_R1_001			0.8%	7.0%	46.2%	44%	151 bp	17%	10.6
P12108_222_S97_L002_R2_001					41.8%	43%	151 bp	42%	11.9
P12108_222_S97_L002_sortmerna_trimmomatic	78.6%	6.1
P12108_223_S98_L002_R1_001			0.7%	5.9%	47.3%	43%	151 bp	8%	12.2
P12108_223_S98_L002_R2_001					43.7%	43%	151 bp	17%	13.3
P12108_223_S98_L002_sortmerna_trimmomatic	80.8%	8.1
P12108_224_S99_L002_R1_001			0.8%	5.3%	51.9%	44%	151 bp	25%	13.6
P12108_224_S99_L002_R2_001					47.8%	43%	151 bp	25%	14.8
P12108_224_S99_L002_sortmerna_trimmomatic	80.2%	8.3
P12108_225_S100_L002_R1_001			0.9%	9.0%	50.2%	44%	151 bp	25%	11.7
P12108_225_S100_L002_R2_001					52.1%	45%	151 bp	33%	13.2
P12108_225_S100_L002_sortmerna_trimmomatic	80.8%	6.9
P12108_226_S101_L002_R1_001			0.7%	5.5%	44.5%	43%	151 bp	17%	10.9
P12108_226_S101_L002_R2_001					39.0%	42%	151 bp	42%	12.2
P12108_226_S101_L002_sortmerna_trimmomatic	78.0%	6.7
P12108_227_S102_L002_R1_001			0.7%	6.3%	54.9%	44%	151 bp	25%	14.8
P12108_227_S102_L002_R2_001					54.8%	44%	151 bp	33%	16.2
P12108_227_S102_L002_sortmerna_trimmomatic	82.3%	9.5
P12108_228_S103_L002_R1_001			0.8%	7.4%	54.4%	45%	151 bp	25%	12.5
P12108_228_S103_L002_R2_001					50.2%	44%	151 bp	50%	14.1
P12108_228_S103_L002_sortmerna_trimmomatic	79.7%	7.4
P12108_229_S104_L002_R1_001			0.6%	7.1%	52.1%	44%	151 bp	25%	12.0
P12108_229_S104_L002_R2_001					53.0%	44%	151 bp	25%	13.2
P12108_229_S104_L002_sortmerna_trimmomatic	82.0%	8.0
P12108_230_S105_L002_R1_001			0.7%	6.6%	53.5%	44%	151 bp	25%	12.4
P12108_230_S105_L002_R2_001					50.4%	44%	151 bp	33%	13.7
P12108_230_S105_L002_sortmerna_trimmomatic	81.0%	7.7
P12108_231_S106_L002_R1_001			0.8%	7.8%	48.3%	44%	151 bp	17%	11.1
P12108_231_S106_L002_R2_001					44.2%	43%	151 bp	42%	12.6
P12108_231_S106_L002_sortmerna_trimmomatic	78.1%	6.4
P12108_232_S107_L002_R1_001			0.7%	9.4%	54.0%	45%	151 bp	25%	11.1
P12108_232_S107_L002_R2_001					50.7%	44%	151 bp	42%	12.7
P12108_232_S107_L002_sortmerna_trimmomatic	80.5%	7.0
P12108_233_S108_L002_R1_001			0.7%	8.2%	54.5%	44%	151 bp	33%	8.4
P12108_233_S108_L002_R2_001					50.3%	44%	151 bp	33%	9.5
P12108_233_S108_L002_sortmerna_trimmomatic	82.8%	5.3
P12108_234_S109_L002_R1_001			0.7%	3.8%	47.3%	43%	151 bp	25%	11.8
P12108_234_S109_L002_R2_001					46.8%	43%	151 bp	33%	12.7
P12108_234_S109_L002_sortmerna_trimmomatic	75.8%	7.2
P12108_235_S110_L002_R1_001			0.7%	3.3%	48.7%	43%	151 bp	17%	13.5
P12108_235_S110_L002_R2_001					48.0%	43%	151 bp	25%	14.3
P12108_235_S110_L002_sortmerna_trimmomatic	76.7%	8.5
P12108_236_S111_L002_R1_001			0.7%	2.0%	62.5%	44%	151 bp	33%	39.9
P12108_236_S111_L002_R2_001					61.8%	44%	151 bp	25%	41.3
P12108_236_S111_L002_sortmerna_trimmomatic	77.5%	25.4
P12108_237_S112_L002_R1_001			0.5%	3.0%	46.9%	43%	151 bp	17%	14.0
P12108_237_S112_L002_R2_001					46.4%	43%	151 bp	25%	14.8
P12108_237_S112_L002_sortmerna_trimmomatic	77.6%	9.5
P12108_238_S113_L002_R1_001			0.7%	2.4%	60.0%	43%	151 bp	33%	30.1
P12108_238_S113_L002_R2_001					55.2%	43%	151 bp	33%	31.5
P12108_238_S113_L002_sortmerna_trimmomatic	79.4%	19.2
P12108_239_S114_L002_R1_001			0.7%	3.4%	50.0%	43%	151 bp	25%	14.8
P12108_239_S114_L002_R2_001					44.3%	43%	151 bp	33%	15.8
P12108_239_S114_L002_sortmerna_trimmomatic	76.7%	9.1
P12108_240_S115_L002_R1_001			0.7%	4.3%	44.8%	43%	151 bp	25%	12.1
P12108_240_S115_L002_R2_001					44.1%	43%	151 bp	42%	13.2
P12108_240_S115_L002_sortmerna_trimmomatic	75.6%	7.1
P12108_241_S116_L002_R1_001			0.7%	4.1%	50.3%	43%	151 bp	17%	13.1
P12108_241_S116_L002_R2_001					43.8%	43%	151 bp	33%	14.2
P12108_241_S116_L002_sortmerna_trimmomatic	76.2%	8.0
P12108_242_S117_L002_R1_001			0.7%	3.1%	44.3%	43%	151 bp	17%	12.6
P12108_242_S117_L002_R2_001					44.1%	43%	151 bp	17%	13.3
P12108_242_S117_L002_sortmerna_trimmomatic	78.1%	8.1
P12108_243_S118_L002_R1_001			0.7%	3.8%	45.0%	43%	151 bp	17%	11.9
P12108_243_S118_L002_R2_001					44.7%	43%	151 bp	33%	12.7
P12108_243_S118_L002_sortmerna_trimmomatic	76.9%	7.5
P12108_244_S119_L002_R1_001			0.7%	4.6%	44.9%	43%	151 bp	17%	12.1
P12108_244_S119_L002_R2_001					44.4%	43%	151 bp	33%	13.2
P12108_244_S119_L002_sortmerna_trimmomatic	76.1%	7.6
P12108_245_S120_L002_R1_001			0.7%	4.2%	46.4%	43%	151 bp	17%	14.7
P12108_245_S120_L002_R2_001					46.1%	43%	151 bp	33%	15.9
P12108_245_S120_L002_sortmerna_trimmomatic	75.9%	9.0
P12108_246_S121_L002_R1_001			0.7%	4.5%	54.9%	43%	151 bp	17%	20.2
P12108_246_S121_L002_R2_001					48.3%	43%	151 bp	33%	22.0
P12108_246_S121_L002_sortmerna_trimmomatic	76.6%	12.7
P12108_247_S122_L002_R1_001			0.7%	4.2%	45.3%	43%	151 bp	17%	16.3
P12108_247_S122_L002_R2_001					45.0%	43%	151 bp	33%	17.7
P12108_247_S122_L002_sortmerna_trimmomatic	76.6%	10.0
P12108_248_S123_L002_R1_001			0.6%	3.0%	42.9%	43%	151 bp	17%	12.4
P12108_248_S123_L002_R2_001					42.6%	43%	151 bp	25%	13.1
P12108_248_S123_L002_sortmerna_trimmomatic	79.6%	8.5
P12108_249_S57_L001_R1_001			0.6%	2.8%	50.2%	43%	151 bp	33%	20.3
P12108_249_S57_L001_R2_001					49.6%	43%	151 bp	33%	21.3
P12108_249_S57_L001_sortmerna_trimmomatic	77.8%	12.9
P12108_250_S58_L001_R1_001			0.6%	3.1%	45.4%	43%	151 bp	17%	15.1
P12108_250_S58_L001_R2_001					44.9%	43%	151 bp	25%	16.0
P12108_250_S58_L001_sortmerna_trimmomatic	78.5%	9.8
P12108_251_S59_L001_R1_001			0.6%	2.8%	49.8%	43%	151 bp	17%	13.1
P12108_251_S59_L001_R2_001					45.7%	43%	151 bp	25%	13.8
P12108_251_S59_L001_sortmerna_trimmomatic	78.5%	8.5
P12108_252_S60_L001_R1_001			0.7%	4.7%	40.5%	43%	151 bp	17%	9.9
P12108_252_S60_L001_R2_001					40.1%	42%	151 bp	42%	10.9
P12108_252_S60_L001_sortmerna_trimmomatic	77.3%	5.7
P12108_253_S61_L001_R1_001			0.6%	2.4%	46.7%	43%	151 bp	17%	11.5
P12108_253_S61_L001_R2_001					42.9%	43%	151 bp	8%	12.0
P12108_253_S61_L001_sortmerna_trimmomatic	79.0%	7.6
P12108_254_S62_L001_R1_001			0.6%	2.5%	50.9%	43%	151 bp	33%	15.9
P12108_254_S62_L001_R2_001					46.1%	43%	151 bp	25%	16.6
P12108_254_S62_L001_sortmerna_trimmomatic	79.5%	10.3
P12108_255_S63_L001_R1_001			0.5%	4.7%	55.0%	44%	151 bp	17%	12.5
P12108_255_S63_L001_R2_001					49.0%	43%	151 bp	33%	13.7
P12108_255_S63_L001_sortmerna_trimmomatic	80.5%	8.4
P12108_256_S64_L001_R1_001			0.6%	5.7%	52.3%	44%	151 bp	17%	10.9
P12108_256_S64_L001_R2_001					46.2%	43%	151 bp	33%	12.2
P12108_256_S64_L001_sortmerna_trimmomatic	79.5%	7.0
P12108_257_S65_L001_R1_001			0.6%	5.5%	49.8%	44%	151 bp	17%	9.1
P12108_257_S65_L001_R2_001					43.6%	43%	151 bp	42%	10.1
P12108_257_S65_L001_sortmerna_trimmomatic	78.8%	5.7
P12108_258_S66_L001_R1_001			0.6%	2.7%	52.3%	44%	151 bp	25%	12.5
P12108_258_S66_L001_R2_001					47.9%	43%	151 bp	33%	13.1
P12108_258_S66_L001_sortmerna_trimmomatic	79.5%	8.0
P12108_259_S67_L001_R1_001			0.9%	4.6%	45.7%	44%	151 bp	17%	8.8
P12108_259_S67_L001_R2_001					41.1%	43%	151 bp	42%	9.7
P12108_259_S67_L001_sortmerna_trimmomatic	76.1%	4.6
P12108_260_S68_L001_R1_001			0.6%	4.1%	52.7%	44%	151 bp	25%	13.5
P12108_260_S68_L001_R2_001					47.4%	43%	151 bp	33%	14.6
P12108_260_S68_L001_sortmerna_trimmomatic	76.6%	8.3
P12108_261_S124_L002_R1_001			0.8%	4.6%	47.5%	44%	151 bp	17%	8.5
P12108_261_S124_L002_R2_001					41.7%	43%	151 bp	33%	9.3
P12108_261_S124_L002_sortmerna_trimmomatic	77.0%	5.2
P12108_262_S125_L002_R1_001			0.8%	4.8%	52.9%	44%	151 bp	25%	12.1
P12108_262_S125_L002_R2_001					46.5%	43%	151 bp	42%	13.3
P12108_262_S125_L002_sortmerna_trimmomatic	77.0%	6.8
P12108_263_S126_L002_R1_001			0.8%	4.0%	47.0%	44%	151 bp	17%	9.4
P12108_263_S126_L002_R2_001					46.1%	43%	151 bp	17%	10.1
P12108_263_S126_L002_sortmerna_trimmomatic	80.4%	6.1

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	Salmon	% Aligned	% Mapped reads	`percent_mapped`	None
\|\|	Salmon	M Aligned	Mapped reads (millions)	`num_mapped`	read_count
\|\|	Trimmomatic	% Dropped	% Dropped reads	`dropped_pct`	None
\|\|	SortMeRNA	% rRNA	Percentage of reads matched to a SortMeRNA database	`rRNA_pct`	None
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

Salmon

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Trimmomatic

Trimmomatic is a flexible read trimming tool for Illumina NGS data.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

SortMeRNA

SortMeRNA is a program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

Sequence Counts

Sequence counts for each sample. Duplicate read counts are an estimate only.

This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Quality Histograms

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

To see the data as a line plot, as in the original FastQC graph, click on a sample track.

From the FastQC help:

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Base N Content

The percentage of base calls at each position for which an N was called.

From the FastQC help:

If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Length Distribution

All samples have sequences of a single length (151bp).

Sequence Duplication Levels

The relative level of duplication found for every sequence.

From the FastQC Help:

In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Overrepresented sequences

The total amount of overrepresented sequences found in each library.

FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

From the FastQC Help:

A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

v1.7

MultiQC Toolbox

Highlight Samples

Rename Samples

Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

General Statistics

Salmon

Trimmomatic

SortMeRNA

FastQC

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Rollover for sample name

Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

Toggle navigation v1.7

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

General Statistics

General Statistics: Columns

Salmon

Trimmomatic

SortMeRNA

FastQC

Sequence Counts Help

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Per Base N Content Help

Sequence Length Distribution

Sequence Duplication Levels Help

Overrepresented sequences Help

Adapter Content Help

v1.7

Highlight Samples

Rename Samples

Show / Hide Samples

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Per Base N Content

Sequence Duplication Levels

Overrepresented sequences

Adapter Content